JAL-1641 updated json schema to make it more generic in order to accomodate more...

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 3a3b665..ff55400 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -35,7 +35,7 @@ public class BioJsHTMLOutput
   public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
           .getDefault(
                   "biojs_template_git_repo",
-                  "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");;
+                  "https://raw.githubusercontent.com/tcofoegbu/bjs-template/master/package.json");
 
   public BioJsHTMLOutput(AlignmentPanel ap,
           FeatureRenderer fr1)

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 30383f3..5e2139e 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -27,15 +27,15 @@ import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.json.binding.v1.AlignmentAnnotationPojo;
 import jalview.json.binding.v1.AlignmentPojo;
+import jalview.json.binding.v1.AlignmentPojo.JalviewBioJsColorSchemeMapper;
 import jalview.json.binding.v1.AnnotationPojo;
-import jalview.json.binding.v1.JalviewSettingsPojo;
-import jalview.json.binding.v1.JalviewSettingsPojo.JalviewBioJsColorSchemeMapper;
 import jalview.json.binding.v1.SequenceFeaturesPojo;
 import jalview.json.binding.v1.SequenceGrpPojo;
 import jalview.json.binding.v1.SequencePojo;
@@ -58,9 +58,11 @@ public class JSONFile extends AlignFile
 {
   private ColourSchemeI colourScheme;
 
-  private String jalviewVersion;
+  private String version = "2.9";
 
-  private String webStartLaunchServletUrl;
+  private String webstartUrl = "www.jalview.org/services/launchApp";
+
+  private String application = "Jalview";
 
   public static final String FILE_EXT = "json";
 
@@ -150,15 +152,21 @@ public class JSONFile extends AlignFile
 
       if (jsonExportSettings.isExportJalviewSettings())
       {
-        jalviewVersion = "";
-        webStartLaunchServletUrl = "www.jalview.org/services/launchApp";
-
-        JalviewSettingsPojo jvSettings = new JalviewSettingsPojo();
-        jvSettings.setGlobalColorScheme(globalColorScheme);
-        jvSettings.setJalviewVersion(jalviewVersion);
-        jvSettings.setWebStartUrl(webStartLaunchServletUrl);
-        jvSettings.setShowSeqFeatures(showSeqFeatures);
-        jsonAlignmentPojo.setJalviewSettings(jvSettings);
+        jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+        jsonAlignmentPojo.getAppSettings().put("application", application);
+        jsonAlignmentPojo.getAppSettings().put("version", version);
+        jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
+        jsonAlignmentPojo.getAppSettings().put("showSeqFeatures",
+                String.valueOf(showSeqFeatures));
+
+        String[] hiddenSections = exportHiddenSections();
+        if (hiddenSections != null)
+        {
+          jsonAlignmentPojo.getAppSettings().put("hiddenCols",
+                  String.valueOf(hiddenSections[0]));
+          jsonAlignmentPojo.getAppSettings().put("hiddenSeqs",
+                  String.valueOf(hiddenSections[1]));
+        }
       }
 
       if (jsonExportSettings.isExportAnnotations())
@@ -209,6 +217,60 @@ public class JSONFile extends AlignFile
     return jsonOutput;
   }
 
+  public String[] exportHiddenSections()
+  {
+    String[] hiddenSections = new String[2];
+    if (getViewport() == null)
+    {
+      return null;
+    }
+
+    System.out.println("--- Hidden Sections ---");
+    // hidden column business
+    if (getViewport().hasHiddenColumns())
+    {
+      System.out.print("Hidden Cols : ");
+      List<int[]> hiddenCols = getViewport().getColumnSelection()
+              .getHiddenColumns();
+      StringBuilder hiddenColsBuilder = new StringBuilder();
+      for (int[] range : hiddenCols)
+      {
+        hiddenColsBuilder.append(";").append(range[0]).append("-")
+                .append(range[1]);
+      }
+
+      hiddenColsBuilder.deleteCharAt(0);
+      hiddenSections[0] = hiddenColsBuilder.toString();
+      System.out.println(hiddenSections[0]);
+    }
+
+    // hidden rows/seqs business
+    HiddenSequences hiddenSeqsObj = getViewport().getAlignment()
+            .getHiddenSequences();
+    if (hiddenSeqsObj == null)
+    {
+      return hiddenSections;
+    }
+
+    SequenceI[] hiddenSeqs = hiddenSeqsObj.hiddenSequences;
+    System.out.print("Hidden Seqs : ");
+    StringBuilder hiddenSeqsBuilder = new StringBuilder();
+    for (SequenceI hiddenSeq : hiddenSeqs)
+    {
+      if (hiddenSeq != null)
+      {
+        hiddenSeqsBuilder.append(";").append(hiddenSeq.hashCode());
+      }
+    }
+    if (hiddenSeqsBuilder.length() > 0)
+    {
+      hiddenSeqsBuilder.deleteCharAt(0);
+    }
+    hiddenSections[1] = hiddenSeqsBuilder.toString();
+    System.out.println(hiddenSections[1]);
+    return hiddenSections;
+  }
+
   public static List<SequenceFeaturesPojo> sequenceFeatureToJsonPojo(
           List<SequenceI> seqs, FeatureRenderer fr)
   {
@@ -304,7 +366,7 @@ public class JSONFile extends AlignFile
       JSONArray seqGrpJsonArray = (JSONArray) alignmentJsonObj
               .get("seqGroups");
       JSONObject jvSettingsJsonObj = (JSONObject) alignmentJsonObj
-              .get("jalviewSettings");
+              .get("appSettings");
 
       if (jvSettingsJsonObj != null)
       {

diff --git a/src/jalview/json/binding/v1/AlignmentPojo.java b/src/jalview/json/binding/v1/AlignmentPojo.java
index b3189c0..9f129f7 100644 (file)
--- a/src/jalview/json/binding/v1/AlignmentPojo.java
+++ b/src/jalview/json/binding/v1/AlignmentPojo.java
@@ -1,6 +1,21 @@
 package jalview.json.binding.v1;
 
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAInteractionColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 
 public class AlignmentPojo
@@ -15,7 +30,7 @@ public class AlignmentPojo
 
   private List<SequenceFeaturesPojo> seqFeatures = new ArrayList<SequenceFeaturesPojo>();
 
-  private JalviewSettingsPojo jalviewSettings;
+  HashMap<String, String> appSettings = new HashMap<String, String>();
 
   public AlignmentPojo()
   {
@@ -31,14 +46,14 @@ public class AlignmentPojo
     this.seqs = seqs;
   }
 
-  public JalviewSettingsPojo getJalviewSettings()
+  public HashMap<String, String> getAppSettings()
   {
-    return jalviewSettings;
+    return appSettings;
   }
 
-  public void setJalviewSettings(JalviewSettingsPojo jalviewSettings)
+  public void setAppSettings(HashMap<String, String> appSettings)
   {
-    this.jalviewSettings = jalviewSettings;
+    this.appSettings = appSettings;
   }
 
   public List<AlignmentAnnotationPojo> getAlignAnnotation()
@@ -76,4 +91,78 @@ public class AlignmentPojo
   {
     return svid;
   }
+
+  public void setGlobalColorScheme(String globalColorScheme)
+  {
+    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
+            .values())
+    {
+      if (cs.getJalviewName().equals(globalColorScheme))
+      {
+        // this.globalColorScheme = cs.getBioJsName();
+        this.appSettings.put("globalColorScheme", cs.getBioJsName());
+        break;
+      }
+    }
+  }
+
+  public enum JalviewBioJsColorSchemeMapper
+  {
+    USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
+            null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
+            "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
+            new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
+            "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
+            "Purine/Pyrimidine", "purine",
+            new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
+            "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
+            "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
+            "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
+            "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
+            "Hydrophobic", "hydro", new HydrophobicColourScheme()),
+
+    // The color types below are not yet supported by BioJs MSA viewer
+    T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
+            "RNA Interaction type", "RNA Interaction type",
+            new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
+            "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
+            "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
+            "% Identity", "pid", new PIDColourScheme());
+
+    private String jalviewName;
+
+    private String bioJsName;
+
+    private ColourSchemeI jvColourScheme;
+
+    private JalviewBioJsColorSchemeMapper(String jalviewName,
+            String bioJsName, ColourSchemeI jvColourScheme)
+    {
+      this.jalviewName = jalviewName;
+      this.bioJsName = bioJsName;
+      this.setJvColourScheme(jvColourScheme);
+    }
+
+    public String getJalviewName()
+    {
+      return jalviewName;
+    }
+
+    public String getBioJsName()
+    {
+      return bioJsName;
+    }
+
+    public ColourSchemeI getJvColourScheme()
+    {
+      return jvColourScheme;
+    }
+
+    public void setJvColourScheme(ColourSchemeI jvColourScheme)
+    {
+      this.jvColourScheme = jvColourScheme;
+    }
+
+  }
+
 }

diff --git a/src/jalview/json/binding/v1/AppSettingsPojo.java b/src/jalview/json/binding/v1/AppSettingsPojo.java
new file mode 100644 (file)
index 0000000..cfc9347
--- /dev/null
+++ b/src/jalview/json/binding/v1/AppSettingsPojo.java
@@ -0,0 +1,91 @@
+package jalview.json.binding.v1;
+
+
+public class AppSettingsPojo
+{
+  // private String globalColorScheme = "none";
+
+  
+
+  public AppSettingsPojo()
+  {
+
+  }
+
+  //
+  //
+  // public void setGlobalColorScheme(String globalColorScheme)
+  // {
+  // for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
+  // .values())
+  // {
+  // if (cs.getJalviewName().equals(globalColorScheme))
+  // {
+  // // this.globalColorScheme = cs.getBioJsName();
+  // this.settings.put("globalColorScheme", cs.getBioJsName());
+  // break;
+  // }
+  // }
+  // }
+  //
+  // public enum JalviewBioJsColorSchemeMapper
+  // {
+  // USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
+  // null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
+  // "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
+  // new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
+  // "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
+  // "Purine/Pyrimidine", "purine",
+  // new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
+  // "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
+  // "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
+  // "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
+  // "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
+  // "Hydrophobic", "hydro", new HydrophobicColourScheme()),
+  //
+  // // The color types below are not yet supported by BioJs MSA viewer
+  // T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
+  // "RNA Interaction type", "RNA Interaction type",
+  // new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
+  // "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
+  // "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
+  // "% Identity", "pid", new PIDColourScheme());
+  //
+  // private String jalviewName;
+  //
+  // private String bioJsName;
+  //
+  // private ColourSchemeI jvColourScheme;
+  //
+  // private JalviewBioJsColorSchemeMapper(String jalviewName,
+  // String bioJsName, ColourSchemeI jvColourScheme)
+  // {
+  // this.jalviewName = jalviewName;
+  // this.bioJsName = bioJsName;
+  // this.setJvColourScheme(jvColourScheme);
+  // }
+  //
+  // public String getJalviewName()
+  // {
+  // return jalviewName;
+  // }
+  //
+  // public String getBioJsName()
+  // {
+  // return bioJsName;
+  // }
+  //
+  // public ColourSchemeI getJvColourScheme()
+  // {
+  // return jvColourScheme;
+  // }
+  //
+  // public void setJvColourScheme(ColourSchemeI jvColourScheme)
+  // {
+  // this.jvColourScheme = jvColourScheme;
+  // }
+  //
+  // }
+
+
+}

diff --git a/src/jalview/json/binding/v1/JalviewSettingsPojo.java b/src/jalview/json/binding/v1/JalviewSettingsPojo.java
deleted file mode 100644 (file)
index 595234c..0000000
--- a/src/jalview/json/binding/v1/JalviewSettingsPojo.java
+++ /dev/null
@@ -1,158 +0,0 @@
-package jalview.json.binding.v1;
-
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAInteractionColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-
-public class JalviewSettingsPojo
-{
-  private String svid = "1.0";
-
-  private String globalColorScheme = "none";
-
-  private String jalviewVersion;
-
-  private String webStartUrl;
-
-  private boolean showSeqFeatures;
-
-  private boolean wrapModeEnabled;
-
-  public JalviewSettingsPojo()
-  {
-
-  }
-
-  public String getGlobalColorScheme()
-  {
-    return globalColorScheme;
-  }
-
-  public void setGlobalColorScheme(String globalColorScheme)
-  {
-    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-            .values())
-    {
-      if (cs.getJalviewName().equals(globalColorScheme))
-      {
-        this.globalColorScheme = cs.getBioJsName();
-        break;
-      }
-    }
-  }
-
-  public String getJalviewVersion()
-  {
-    return jalviewVersion;
-  }
-
-  public void setJalviewVersion(String jalviewVersion)
-  {
-    this.jalviewVersion = jalviewVersion;
-  }
-
-  public String getWebStartUrl()
-  {
-    return webStartUrl;
-  }
-
-  public void setWebStartUrl(String webStartUrl)
-  {
-    this.webStartUrl = webStartUrl;
-  }
-
-  public boolean isShowSeqFeatures()
-  {
-    return showSeqFeatures;
-  }
-
-  public void setShowSeqFeatures(boolean showSeqFeatures)
-  {
-    this.showSeqFeatures = showSeqFeatures;
-  }
-
-  public boolean isWrapModeEnabled()
-  {
-    return wrapModeEnabled;
-  }
-
-  public void setWrapModeEnabled(boolean wrapModeEnabled)
-  {
-    this.wrapModeEnabled = wrapModeEnabled;
-  }
-
-  public enum JalviewBioJsColorSchemeMapper
-  {
-    USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
-            null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
-            "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
-            new TaylorColourScheme()), NUCLEOTIDE("Nucleotide",
-            "nucleotide", new NucleotideColourScheme()), PURINE_PYRIMIDINE(
-            "Purine/Pyrimidine", "purine",
-            new PurinePyrimidineColourScheme()), HELIX_PROPENCITY(
-            "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
-            "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
-            "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
-            "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
-            "Hydrophobic", "hydro", new HydrophobicColourScheme()),
-
-    // The color types below are not yet supported by BioJs MSA viewer
-    T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
-            "RNA Interaction type", "RNA Interaction type",
-            new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
-            "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
-            "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
-            "% Identity", "pid", new PIDColourScheme());
-
-    private String jalviewName;
-
-    private String bioJsName;
-
-    private ColourSchemeI jvColourScheme;
-
-    private JalviewBioJsColorSchemeMapper(String jalviewName,
-            String bioJsName, ColourSchemeI jvColourScheme)
-    {
-      this.jalviewName = jalviewName;
-      this.bioJsName = bioJsName;
-      this.setJvColourScheme(jvColourScheme);
-    }
-
-    public String getJalviewName()
-    {
-      return jalviewName;
-    }
-
-    public String getBioJsName()
-    {
-      return bioJsName;
-    }
-
-    public ColourSchemeI getJvColourScheme()
-    {
-      return jvColourScheme;
-    }
-
-    public void setJvColourScheme(ColourSchemeI jvColourScheme)
-    {
-      this.jvColourScheme = jvColourScheme;
-    }
-
-  }
-
-  public String getSvid()
-  {
-    return svid;
-  }
-
-}